API for DECIPHER
Tools for curating, analyzing, and manipulating biological sequences

Global functions
.CalculateEfficiencyFISH	Source code
.CalculateEfficiencyPCR	Source code
.NNI	Source code
.append	Source code
.applyMidpoints	Source code
.centerPoint	Source code
.chainGenes	Source code
.collapse	Source code
.extractRBS	Source code
.logisticRegression	Source code
.onUnload	Source code
.optimizeModel	Source code
.organizeClusters	Source code
.organizeClustersFast	Source code
.performFolding	Source code
.plotIDs	Source code
.primerDimer	Source code
.rates	Source code
.reorderClusters	Source code
.replace	Source code
.root	Source code
.simultaneousBrent	Source code
.splitClusters	Source code
.spoke	Source code
.sqliteDataType	Source code
.subset	Source code
.swapBranches	Source code
.switch	Source code
.tiledTemplate	Source code
AA_REDUCED	Man page
Add2DB	Man page Source code
AdjustAlignment	Man page Source code
AlignDB	Man page Source code
AlignProfiles	Man page Source code
AlignSeqs	Man page Source code
AlignSynteny	Man page Source code
AlignTranslation	Man page Source code
AmplifyDNA	Man page Source code
Array2Matrix	Man page Source code
BrowseDB	Man page Source code
BrowseSeqs	Man page Source code
CalculateEfficiencyArray	Man page Source code
CalculateEfficiencyFISH	Man page Source code
CalculateEfficiencyPCR	Man page Source code
Codec	Man page Source code
ConsensusSequence	Man page Source code
Cophenetic	Man page Source code
CorrectFrameshifts	Man page Source code
CreateChimeras	Man page Source code
DB2Seqs	Man page Source code
DECIPHER	Man page
DECIPHER-package	Man page
DesignArray	Man page Source code
DesignPrimers	Man page Source code
DesignProbes	Man page Source code
DesignSignatures	Man page Source code
DigestDNA	Man page Source code
Disambiguate	Man page Source code
DistanceMatrix	Man page Source code
ExtractGenes	Man page Source code
FindChimeras	Man page Source code
FindGenes	Man page Source code
FindSynteny	Man page Source code
FormGroups	Man page Source code
Genes-class	Man page
HEC_MI1	Man page
HEC_MI2	Man page
IdClusters	Man page Source code
IdConsensus	Man page Source code
IdLengths	Man page Source code
IdTaxa	Man page Source code
IdentifyByRank	Man page Source code
LearnTaxa	Man page Source code
MIQS	Man page
MODELS	Man page
MapCharacters	Man page Source code
MaskAlignment	Man page Source code
MeltDNA	Man page Source code
NNLS	Man page Source code
OrientNucleotides	Man page Source code
PFASUM	Man page
PredictDBN	Man page Source code
PredictHEC	Man page Source code
RESTRICTION_ENZYMES	Man page
ReadDendrogram	Man page Source code
RemoveGaps	Man page Source code
SearchDB	Man page Source code
Seqs2DB	Man page Source code
StaggerAlignment	Man page Source code
Synteny-class	Man page
Taxa-class	Man page
TerminalChar	Man page Source code
TileSeqs	Man page Source code
TrainingSet_16S	Man page
TrimDNA	Man page Source code
WriteDendrogram	Man page Source code
WriteGenes	Man page Source code
[.Genes	Man page
[.Synteny	Man page
[.Taxa	Man page
`.substr<-`	Source code
`[.Genes`	Source code
`[.Synteny`	Source code
`[.Taxa`	Source code
`c.Taxa`	Source code
c.Taxa	Man page
deltaGrules	Man page
deltaHrules	Man page
deltaHrulesRNA	Man page
deltaSrules	Man page
deltaSrulesRNA	Man page
pairs.Synteny	Man page Source code
plot.Genes	Man page Source code
plot.Synteny	Man page Source code
plot.Taxa	Man page Source code
print.Genes	Man page Source code
print.Synteny	Man page Source code
print.Taxa	Man page Source code
to.dendrogram	Source code